MBGD is a database system for making use of rapidly accumulating microbial genome sequences through comparative analysis. The basic function of MBGD is to create an orthologous gene classification table, which comprises sets of "equivalent" genes among multiple genomes. In MBGD, classification tables can be created on demand with specified set of organisms and parameters. This feature becomes important to understand diversity of genomes using almost a hundred genome sequences now available.
DIGIT is a computer program which finds genes by combining plural existing gene-finders. The comprehensive benchmark tests clearly showed that DIGIT whose model parameters were optimized for combining human ab initio gene-finders successfully discarded many false-positive exons predicted by the gene-finders and yielded remarkable improvements in prediction accuracy compared with existing ab initio gene-finder. In this paper, I introduce the use of DIGIT via internet as well as the outline of DIGIT algorithm.
3DinSight is an integrated database and search tool for the structure, property and function of biomolecules. 3DinSight consists of an integrated database, a set of search programs, a WWW interface and visualization tools. It has been open to public through the Internet. 3DinSight would help researchers to get insight into the relationship among the structure, property and function of biomolecules.
We have developed the database, "ProTherm:Thermodynamic Database for Proteins and Mutants," which contains more than 11,000 numerical data for several important thermodynamic properties, structural information of proteins and mutants, experimental methods and conditions, and, functional and literature information. ProTherm can be searched through WWW on various conditions with different options for output. In addition, it is cross-linked with structure, function and literature databases such as PDB, PMD, ENZYME, SWISS-PROT, PIR and PubMed. The structure of mutation sites and surrounding residues can be directly viewed through 3DinSight, which is developed in our laboratory. ProTherm is freely available at above URL.
Quantitative data of protein-nucleic acid interactions are important for understanding the molecular mechanisms of their recognition and gene regulation. We have developed the database, "ProNIT:Thermodynamic Database for Protein-Nucleic Acid Interactions", which contains numerical data for several experimental binding data, structural information of proteins, nucleic acids and the complex, experimental methods and conditions, and functional and literature information. A WWW interface allows users to search for data based on various conditions, and to visualize molecular structures, properties and their interactions. ProNIT is freely available at above URL.
We developed a computer program, FAMS (Full Automatic Modeling System) to build model structures based on reference structures solved using X-ray diffraction, NMR or other experimental methods, and amino acid sequence alignment between a target and its reference structure. Its ability was clearly shown in the CAFASP2 competition1). FAMS produces a model whose torsion angles of the backbone and sidechain are highly accurate. The processes of the FAMS algorithm are fully automated and therefore don't require any special knowledge, techniques or experience to obtain a biologically worthwhile protein structure.
The observed kinetics of protein folding is a consequence of averaging over an ensemble of many activated barrier crossings with multiple time scales. The future of the recent remarkable experimental developments in single molecule spectroscopy holds great promise to reveal the complexity of protein folding dynamics. A few theoretical possible means to address and clarify the dynamical complexity such as abnormal diffusion of a protein are presented.
Many organisms including human beings have rhodopsin as photoreceptor. In cell membranes of archaeal Halobacterium salinarum, there exist four rhodopsin-like proteins (so-called archaeal rhodopsins). Two of these work as light-driven ion pumps. The other two work as photosensors and are named sensory rhodopsin (sR) and phoborhodopsin (pR). pR mediates the negative phototaxis. Recently, X-ray crystallographic structure of pR derived from Natronobacterium pharaonis is reported, and allows us to investigate the function-structure relationship at atomic level. In this review, we describe our results on the photochemistry and the signal transduction mechanism of pR.
Toll-like receptors (TLRs) are pattern-recognition receptors that play key roles in detecting microbes and initiating inflammatory responses. Ten members of the TLR family have been identified in humans. TLRs consist of an extracellular domain containing leucine-rich repeats and a C-terminal flanking region, and a cytoplasmic signaling domain, called the Toll/IL-1 receptor homology domain. Each TLR recognizes a distinct ligand (s) and induces different, sometimes overlapping, immune responses. Here, I show that TLR2 recognizes bacterial lipoproteins, while TLR3 recognizes virus-derived double-stranded RNA and triggers downstream signals leading to interferon production.